Variant report

Variant	rs1988708
Chromosome Location	chr11:8882893-8882894
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10743093	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10743095	0.84[EUR][1000 genomes]
rs10769967	0.82[EUR][1000 genomes]
rs10769968	0.96[EUR][1000 genomes]
rs10769970	0.94[EUR][1000 genomes]
rs10769971	0.94[EUR][1000 genomes]
rs10769973	0.94[EUR][1000 genomes]
rs10840130	0.81[EUR][1000 genomes]
rs10840134	0.84[EUR][1000 genomes]
rs10840136	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840141	0.95[EUR][1000 genomes]
rs10840142	0.96[EUR][1000 genomes]
rs10840147	0.94[EUR][1000 genomes]
rs10840148	0.94[EUR][1000 genomes]
rs11042078	0.81[EUR][1000 genomes]
rs11042079	0.81[EUR][1000 genomes]
rs11042082	0.82[EUR][1000 genomes]
rs11042088	0.82[EUR][1000 genomes]
rs11042102	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11042103	0.96[EUR][1000 genomes]
rs11042125	0.81[EUR][1000 genomes]
rs1109305	0.84[EUR][1000 genomes]
rs11603841	0.82[EUR][1000 genomes]
rs1529641	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1560569	0.83[EUR][1000 genomes]
rs1569408	0.95[EUR][1000 genomes]
rs1883098	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1988709	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2016942	0.83[EUR][1000 genomes]
rs2568043	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2568054	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2568059	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568061	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568062	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568065	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568090	0.82[EUR][1000 genomes]
rs2653567	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653593	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653606	0.82[EUR][1000 genomes]
rs2653607	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2653613	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653616	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742536	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2742537	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742540	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742545	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742550	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742552	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34842234	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36192694	0.83[EUR][1000 genomes]
rs4554887	0.82[EUR][1000 genomes]
rs4909952	0.81[EUR][1000 genomes]
rs4910062	0.84[EUR][1000 genomes]
rs4910119	0.95[EUR][1000 genomes]
rs4910156	0.83[EUR][1000 genomes]
rs4910158	0.82[EUR][1000 genomes]
rs4910200	0.81[EUR][1000 genomes]
rs61876187	0.82[EUR][1000 genomes]
rs7118463	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7119939	0.84[EUR][1000 genomes]
rs7123429	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7123861	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7937298	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7943377	0.82[EUR][1000 genomes]
rs978636	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1988708	AKIP1	cis	Thyroid	GTEx
rs1988708	TMEM9B-AS1	cis	lung	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8862400-8885000	Weak transcription	NHLF	lung
2	chr11:8862400-8888400	Weak transcription	Right Atrium	heart
3	chr11:8862600-8885200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:8863200-8890400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:8864000-8888000	Weak transcription	Fetal Intestine Small	intestine
6	chr11:8865800-8886000	Weak transcription	Fetal Stomach	stomach
7	chr11:8873200-8885000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:8874600-8885000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:8877400-8888600	Weak transcription	Fetal Muscle Leg	muscle
10	chr11:8877400-8888600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:8878200-8891800	Weak transcription	Psoas Muscle	Psoas
12	chr11:8879400-8885600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:8879600-8884000	Weak transcription	Ovary	ovary
14	chr11:8880200-8892000	Weak transcription	Gastric	stomach
15	chr11:8880400-8884000	Weak transcription	Left Ventricle	heart
16	chr11:8880400-8885800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:8880400-8888000	Weak transcription	Stomach Mucosa	stomach
18	chr11:8880400-8888200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:8880400-8889200	Weak transcription	Lung	lung
20	chr11:8880600-8884000	Weak transcription	Spleen	Spleen
21	chr11:8880600-8884200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:8880600-8885000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:8880800-8885000	Weak transcription	Placenta	Placenta
24	chr11:8881400-8888200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:8881600-8885000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:8881600-8885000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr11:8881800-8883000	Weak transcription	Colon Smooth Muscle	Colon
28	chr11:8881800-8884400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr11:8882000-8884400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:8882200-8885000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:8882600-8884200	Weak transcription	Hela-S3	cervix
32	chr11:8882800-8883000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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